//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "sharedfile"; inputfile = sharedfile; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
relabundfile = validParameter.validFile(parameters, "relabund", true);
if (relabundfile == "not open") { relabundfile = ""; abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
- else { format = "relabund"; inputfile = relabundfile; }
+ else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
if ((sharedfile == "") && (relabundfile == "")) {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "norm.shared";
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
input = new InputData(inputfile, format);
//you are reading a sharedfile and you do not want to make relabund
m->mothurOut("Normalizing to " + toString(norm) + "."); m->mothurOutEndLine();
}
+
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- normalize(lookup, out);
+ normalize(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- normalize(lookup, out);
+ normalize(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- normalize(lookup, out);
+ normalize(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
//as long as you are not at the end of the file or done wih the lines you want
while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } m->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } m->Groups.clear(); return 0; }
if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
- normalize(lookupFloat, out);
+
+ normalize(lookupFloat);
processedLabels.insert(lookupFloat[0]->getLabel());
userLabels.erase(lookupFloat[0]->getLabel());
for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
- m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
- normalize(lookupFloat, out);
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+
+ normalize(lookupFloat);
processedLabels.insert(lookupFloat[0]->getLabel());
userLabels.erase(lookupFloat[0]->getLabel());
//prevent memory leak
for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
- if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; }
//get next line to process
lookupFloat = input->getSharedRAbundFloatVectors();
}
- if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
- normalize(lookupFloat, out);
+ normalize(lookupFloat);
for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
}
//reset groups parameter
m->Groups.clear();
delete input;
- out.close();
- if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+ //m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set shared file as new current sharedfile
}
//**********************************************************************************************************************
-int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
try {
+ //save mothurOut's binLabels to restore for next label
+ vector<string> saveBinLabels = m->currentBinLabels;
+
if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
if (method == "totalgroup") {
+
+ //save numSeqs since they will change as the data is normalized
+ vector<int> sizes;
+ for (int i = 0; i < thisLookUp.size(); i++) { sizes.push_back(thisLookUp[i]->getNumSeqs()); }
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
for (int i = 0; i < thisLookUp.size(); i++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
int abund = thisLookUp[i]->getAbundance(j);
- float relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+ float relabund = abund / (float) sizes[i];
float newNorm = relabund * norm;
//round to nearest int
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
//calc mean
float mean = 0.0;
eliminateZeroOTUS(thisLookUp);
+
+ thisLookUp[0]->printHeaders(out);
for (int i = 0; i < thisLookUp.size(); i++) {
out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t';
thisLookUp[i]->print(out);
}
+ out.close();
+
+ m->currentBinLabels = saveBinLabels;
+
return 0;
}
catch(exception& e) {
}
//**********************************************************************************************************************
-int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLookUp, ofstream& out){
+int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLookUp){
try {
+
+ //save mothurOut's binLabels to restore for next label
+ vector<string> saveBinLabels = m->currentBinLabels;
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+
+
if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
if (method == "totalgroup") {
+ //save numSeqs since they will change as the data is normalized
+ vector<float> sizes;
+ for (int i = 0; i < thisLookUp.size(); i++) { sizes.push_back(thisLookUp[i]->getNumSeqs()); }
+
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
for (int i = 0; i < thisLookUp.size(); i++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
float abund = thisLookUp[i]->getAbundance(j);
- float relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+ float relabund = abund / (float) sizes[i];
float newNorm = relabund * norm;
thisLookUp[i]->set(j, newNorm, thisLookUp[i]->getGroup());
}else if (method == "zscore") {
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
//calc mean
float mean = 0.0;
eliminateZeroOTUS(thisLookUp);
+ thisLookUp[0]->printHeaders(out);
+
for (int i = 0; i < thisLookUp.size(); i++) {
out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t';
thisLookUp[i]->print(out);
}
+ out.close();
+
+ m->currentBinLabels = saveBinLabels;
+
return 0;
}
catch(exception& e) {
}
//for each bin
+ vector<string> newBinLabels;
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
for (int j = 0; j < thislookup.size(); j++) {
newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
}
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu" + toString(i+1);
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
}
}
for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
return 0;
}
//for each bin
+ vector<string> newBinLabels;
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
for (int j = 0; j < thislookup.size(); j++) {
newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
}
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu" + toString(i+1);
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
}
}
for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
return 0;
projects / mothur.git / blobdiff